Hi David,
3dAutobox is an AFNI command, not an FSL one, so I can't help with that.
However, if you just want a bounding box from a rough brain mask then
fslstats with the -w option is what you want. And it is already in the conventions
needed for fslroi.
All the best,
Mark
On 18 Apr 2012, at 22:12, David Gutman wrote:
> So I've used the fslROI command to manually crop images before.... but I've generally gone in and set the x/y/z min max manually and fed that in.
>
> My specific use case is that I am doing brain extraction and my images have a lot of neck/extra stuff... and are pretty high resolution so I'm trying to shrink my matrix to cut down on memory requirements for subsequent registration steps.
>
>
> I've been using the 3dAutobox command in FSL to automatically generate the bounding box and cropped output file... but I have to run it twice (it moves the brain to the "bottom" on the first pass.. and still leaves a lot of empty space above the extracted brain). More importantly... it's kind of screwing up the header..
>
>
> Basically I want something like "cluster" in FSL that would output the x/y/z bounding box of the brain mask using native FSL commands... In the meantime I've just been grabbing the coordinate 3d-autobox puts out and using that in FSLroi... but I'm seeing if there's a more elegant solution.....
>
>
> dg
>
>
> --
>
> David A Gutman, M.D. Ph.D.
> Assistant Professor of Biomedical Informatics
> Senior Research Scientist, Center for Comprehensive Informatics
> Emory University School of Medicine
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